Detailed Description

Embed a configuration using the XYZ coordinates of a set of particles.

The point for each configuration of the model is a concatenation of the Cartesian coordinates of the particles contained in the passed SingletonContainer.

See ConfigurationSet for more information about the input.

import IMP.example
import IMP.statistics
(m,c)=IMP.example.create_model_and_particles()
ps= IMP.core.DistancePairScore(IMP.core.HarmonicLowerBound(1,1))
r= IMP.container.PairsRestraint(ps, IMP.container.ClosePairContainer(c, 2.0))
m.add_restraint(r)
# we don't want to see lots of log messages about restraint evaluation
m.set_log_level(IMP.WARNING)
# the container (c) stores a list of particles, which are alse XYZR particles
# we can construct a list of all the decorated particles
xyzrs= c.get_particles()
s= IMP.core.MCCGSampler(m)
s.set_number_of_attempts(10)
# but we do want something to watch
s.set_log_level(IMP.TERSE)
s.set_number_of_monte_carlo_steps(10)
# find some configurations which move the particles far apart
configs= s.get_sample();
for i in range(0, configs.get_number_of_configurations()):
    configs.load_configuration(i)
    # print out the sphere containing the point set
    # - Why? - Why not?
    sphere= IMP.core.get_enclosing_sphere(xyzrs)
    print sphere
# cluster the solutions based on their coordinates
e= IMP.statistics.ConfigurationSetXYZEmbedding(configs, c)
# of course, this doesn't return anything of interest since the points are
# randomly distributed, but, again, why not?
clustering = IMP.statistics.create_lloyds_kmeans(e, 3, 1000)
for i in range(0,clustering.get_number_of_clusters()):
    # load the configuration for a central point
    configs.load_configuration(clustering.get_cluster_representative(i))
    sphere= IMP.core.get_enclosing_sphere(xyzrs)
    print sphere

Examples: basic optimization, nup84 cg, nup84 rb, analyze 0

Inheritance diagram for IMP::statistics::ConfigurationSetXYZEmbedding:

List of all members.

Public Member Functions
	ConfigurationSetXYZEmbedding (ConfigurationSet cs, SingletonContainer sc, bool align=false)
unsigned int	get_number_of_items () const
algebra::VectorKD	get_point (unsigned int i) const
Public Member Functions inherited from IMP::statistics::Embedding
	Embedding (std::string name)
Public Member Functions inherited from IMP::base::Object
std::size_t	__hash__ () const
virtual std::string	get_type_name () const =0
	Return a string identifying the type of the object.
virtual IMP::base::VersionInfo	get_version_info () const =0
	Get information about the module and version of the object.
void	set_check_level (CheckLevel l)
void	set_log_level (LogLevel l)
	Set the logging level used in this object.
void	set_was_used (bool tf) const
void	show (std::ostream &out=std::cout) const
const std::string &	get_name () const
void	set_name (std::string name)

Static Public Member Functions
static ConfigurationSetXYZEmbedding *	get_from (IMP::base::Object *o)

Constructor & Destructor Documentation

IMP::statistics::ConfigurationSetXYZEmbedding::ConfigurationSetXYZEmbedding	(	ConfigurationSet *	cs,
		SingletonContainer *	sc,
		bool	align = `false`
	)

If align is true, all the configurations are rigidly aligned with the first before generating their coordinates.

The documentation for this class was generated from the following file:

point_clustering.h

Detailed Description

Public Member Functions

Static Public Member Functions

Constructor & Destructor Documentation